I agree with the article, but this ISN'T the case!
You are rebasing "your" private branch, with your history, and before having the merge accepted (if it will be accepted) you can do whatever you want, this won't affect other people at all.
The problem is when everybody uses the same repository, but this isn't how github works, because everyone uses a "private" repository and ask for pull requests (sometimes I directly commit on master here, but I know this is BAD).

So feel free to rebase master and whatever you want, the master won't be affected (and the "merge" line will be there when and if the pull request will be accepted)